Some switches only support one encapsulation type on a trunk. In that case, there is no command "switchport trunk encapsulation dot1q". Some older Cisco stuff only done the proprietary ISL trunking. Now most switches do the standard dot1q or both methods.

If you are using Packet Tracer, it may not support the command switchport trunk encapsulation dot1q, but will still use it as a default. You will still be good to go if you use the switchport mode trunk command.